Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

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概要

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• The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, geneprediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level.Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following:integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates(1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for nonprotein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causingphenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.

• Public Library of Scienceの論文

著者

• Sugano Sumio

  放射線医学総合研究所

• Sugano Sumio

  Helix Research Institute

• Hanada Hironori

  Research Institute National Cardiovascular Center

• Sugano Sumio

  Department Of Virology Institute Of Medical Science University Of Tokyo

• Suzuki Yoichi

  Department Of Medical Genetics Tohoku University School Of Medicine

• NISHIKAWA Ken

  National Institute of Genetics

• Sugano Sumio

  University Of Tokyo

• Miyazaki J

  Univ. Tsukuba Ibaraki Jpn

• Suzuki Yutaka

  University of Tokyo

• Kanai Akinori

  University of Tokyo

• Nakai Kenta

  University of Tokyo

• Yamamoto Takako

  Department Of Health Science Shiga University Of Medical Science

• Yura K

  Department Of Biological Science Graduate School Of Science Nagoya University

• Yura Kei

  Quantum Bioinfo. Jaea

• Ohtsubo Masafumi

  Medical Photobiology Department Photon Medical Research Center Hamamatsu University School Of Medici

• Sakata Yoshiyuki

  Department Of Medical Genetics Tohoku University School Of Medicine

• Osada Naoki

  Division Of Genetic Resources National Institute Of Infectious Diseases

• Suzuki Y

  Department Of Medical Genetics Tohoku University School Of Medicine

• SUZUKI Yasuyo

  Department of Clinical Genetics, Medical Institute of Bioregulation, Kyushu University

• Mashima Jun

  Institute Of Biological Sciences University Of Tsukuba:(present Address)school Of Life Science Unive

• Inoko Hidetoshi

  Dep. Of Molecular Life Sci. Tokai Univ. School Of Medicine

• Go Mitiko

  Fac. Bio-sci. Nagahama Inst. Bio-sci. Tech.:ochanomizu Univ.

• Hanada Kouichi

  Departoment Of Neurology And Geriatrics Kagoshima University Graduate School Of Medical And Dental S

• Suwa Makiko

  Computational Biology Research Center (cbrc) National Institute Of Advanced Industrial Science And T

• Hashimoto Katsuyuki

  Division Of Genetic Resources National Institute Of Infectious Diseases

• Homma Keiichi

  National Institute Of Genetics

• Fukuchi Satoshi

  Maebashi Institute of Technology

• MANO Shuhei

  Nagoya City University

• Shimizu Nobuyoshi

  Department of Molecular Biology, Keio University School of Medicine

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